Publications

Physics/Biophysics

2017

48. Entangled proteins: knots, slipknots, links, and lassos
P Sułkowski, JI Sulkowska
(under review)

47. The exclusive effects of chaperonin on the behavior of the 52 knotted proteins
Y Zhao*, S Niewieczerzal*, P Dabrowski-Tumanski*, JI Sulkowska
(under review)

46. GapRepairer – repair structures with topological care
AI Jarmolinska*, M Kadlof*, P Dabrowski-Tumanski, JI Sulkowska
(under review)

45. Proteins’ knotty problems
AI Jarmolinska, AP Perlinska, R Runkel, B Trefz, P Virnau, JI Sulkowska
(under review)

44. To tie or not to tie? That is the question
P Dabrowski-Tumanski, JI Sulkowska
Polymers in press

43. PyLasso – a PyMOL plugin to identify lassos
A Gierut, W Niemyska, P Dabrowski-Tumanski, P Sułkowski, JI Sulkowska
Bioinformatics in press

42. Knotting and unknotting proteins in the chaperonin cage: effects of the excluded volume
S Niewieczerzal, JI Sulkowska
PloS One (2017) 12(5) doi: 10.1371/journal.pone.0176744

41. TrmD: A Methyl Transferase for tRNA Methylation With m1G37
YM Hou, R Matsubara, R Takase, I Masuda, JI Sulkowska
The Enzymes (2017): doi: 10.1016/bs.enz.2017.03.003

40. Topological knots and links in proteins
P Dabrowski-Tumanski, JI Sulkowska
PNAS (2017): doi: 10.1073/pnas.1615862114

2016

39. Molecular dynamics and structural comparison approach to understanding the role of the knots in proteins
AP Perlinska, JM Macnar, JI Sulkowska
TASK Quarterly (2016) 20: 373-381

38. Current approaches to disentangle the mystery of knotted protein folding
P Dabrowski-Tumanski, M Sklodowski, JI Sulkowska
TASK Quarterly (2016) 20: 361-371

37. In search of functional advantages of knots in proteins
P Dabrowski-Tumanski, A Stasiak, JI Sulkowska
PLoS One (2016) doi: 10.1371/journal.pone.0165986

36. Complex lasso: new entangled motifs in proteins
W Niemyska, P Dabrowski-Tumanski, M Kadlof, E Haglund, P Sułkowski, JI Sulkowska
Scientific Reports (2016) doi: 10.1038/srep36895

35.LinkProt: database collecting information about biological links
P Dabrowski-Tumanski*, AI Jarmolinska*, W Niemyska*, E Rawdon, KC Millett, JI Sulkowska
Nucleic Acids Res. (2016) doi: 10.1093/nar/gkw976

34. Methyl Transfer by Substrate Signaling from a Knotted Protein Fold
T Christian*, R Sakaguchi*, AP Perlinska*, G Lahoud, T Ito, EA Taylor, S Yokoyama, JI Sulkowska, Ya-Ming Hou
Nature Structural & Molecular Biology (2016) 23: 941-948

33. LassoProt: server to analyze biopolymers with lassos
P Dąbrowski-Tumanski, W Niemyska, P Pasznik, JI Sulkowska
Nucleic Acids Res. (2016), doi: 10.1093/nar/gkw308

2015

32. Prediction of the optimal set of contacts to fold the smallest knotted protein
P Dąbrowski-Tumanski, AI Jarmolińska, JI Sułkowska
J. Phys. Cond. Mat. (2015) 27(35):354109. doi: 10.1088/0953-8984/27/35/354109.

2014

31. KnotProt: a database of proteins with knots and slipknots
M Jamroz, W Niemyska, EJ Rawdon, A Stasiak, KC Millett, P Sułkowski, JI Sulkowska
Nucleic Acids Res. (2014), 43: D306-D314.

30. Pierced Lasso Bundles are a New Class of Knot Motifs
E. Haglund, JI Sulkowska, J.K. Noel, H. Lammert, J.N. Onuchic, PA Jennings
PloS Comput. Biology (2014) 19,10(6):e1003613.

29. Determining Critical Amino Acid contacts for knotted protein
P Dabrowski-Tumanski, S Niewieczerzal, JI Sulkowska
TASK Quarterly (2014) 18 No 3, 323–337.

28. Connecting Thermal and Mechanical Protein (Un)folding Landscapes
L Sun, JK Noel, JI Sulkowska, H Levine, JN Onuchic
Biophys J. 16 (2014), 107(12):2941-52

2013

27. Knot localization in proteins
EJ Rawdon, KC Millett, JI Sulkowska, A Stasiak
Biochemical Society Transactions (2013) 41(2):538-41. doi: 10.1042/BST20120329.

26. Identifying knots in proteins
KC Millett, EJ Rawdon, A Stasiak, JI Sulkowska
Biochemical Society Transactions (2013) 41(2):533-7, doi: 10.1042/BST20120339.

25. Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins
T Andrews, DT Capraro, JI Sulkowska, JN Onuchic, PA Jennings
J. Phys. Chemistry Letters (2013) Jan 3;4(1):180-188.

24. Knotting a Protein in Explicit Solvent
JK Noel, JN Onuchic, JI Sulkowska
J. Phys. Chem. Letters (2013) 4(21), 3570-3573.

23. Knotting pathways in proteins
JI Sulkowska, JK Noel, CA Ramírez-Sarmiento, EJ Rawdon, KC Millett, JN Onuchic
Biochemical Society Transactions (2013) 41(2):523-7, doi: 10.1042/BST20120342.

2012

22. Energy landscape of knotted protein folding
JI Sulkowska*, JK Noel*, JN Onuchic
Proc. Natl. Acad. Sci. USA (2012) doi: 10.1073/pnas.1201804109.

21. Conservation of complex knotting and slipknotting patterns in proteins
JI Sulkowska, EJ Rawdon, KC Millett, JN Onuchic, A Stasiak
Proc. Natl. Acad. Sci (USA), (2012) 109(26): E1715-23.

20. The unique cysteine knot regulates the pleotropic hormone leptin
E Haglund, JI Sulkowska, Z He, Gen-Sheng Feng, P Jennings, JN Onuchic
PloS One (2012) 7(9) e45654.

19. Genomics-aided Structure Prediction (GASP)
JI Sulkowska*, F Marcos*, M Weigt, T Hwa, JN Onuchic
Proc. Natl. Acad. Sci. USA (2012), 109(26): 10340-5.

2011

18. BSDB: the biomolecule stretching database
M Sikora, JI Sulkowska, BS Witkowski, M Cieplak
Nucleic Acids Res. (2011) 39:D443-50. doi: 10.1093/nar/gkq851.

17. Structure based models of biomolecules: stretching of proteins, dynamics of knots, hydrodinamic effects, and indentation of virus capsids
M Cieplak, JI Sulkowska
Springer, A. Koliński, Chapter 8, New York, pp. 179-208, DOI 10.1007/978-1- 4419-6889- 0 (2011).

2010

16. Slipknotting upon native-like loop formation in a trefoil knot protein
JK Noel, JI Sulkowska, JN Onuchic
Proc. Natl. Acad. Sci. USA (2010) 107, 15403.

15. Untying knots in proteins
JI Sulkowska, P Sułkowski, P Szymczak, M Cieplak
J. Am. Chem. Soc. 132 (40) (2010) 13954-13956.

14. A Stevedore’s protein knot
D Bölinger*, JI Sulkowska*, HP Hsu, LA Mirny, M Kardar, JN Onuchic, P Virnau
PLoS Comput Biol. (2010) 6, e1000731.

2009

13. Dodging the crisis of folding proteins with knots
JI Sulkowska, P Sułkowski, JN Onuchic
Proc. Natl. Acad. Sci. USA (2009) 106, 3119-3124, arXiv: 0912.5450 [q-bio].

12. Jamming proteins with slipknots and their free energy landscape
JI Sulkowska, P Sułkowski, JN Onuchic
Phys. Rev. Lett. (2009) 103 268103, arXiv: 1001.0009.

11. On the remarkable mechanostability of scaffoldins and the mechanical clamp motif
A Valbuena, J Oroz, R Hervas, AM Vera, D Rodrigues, A Menedez, JI Sulkowska, M Cieplak, M Carrion-Vazquez
Proc. Natl. Acad. Sci. (2009) 106, 13791.

10. Mechanical strength of 17 134 model proteins and cysteine slipknots motive
M Sikora*, JI Sulkowska*, M Cieplak
PLoS Comput. Biol. (2009) 5, e1000547.

9. Tests of the Structure-Based Models of Proteins
M Cieplak, JI Sulkowska
Act. Phys Polonica A (2009) 115, 441.

2008

8. Stabilizing effect of knots on proteins – How knots influence properties of proteins
JI Sulkowska, P Sułkowski, P Szymczak, M Cieplak
PNAS 105 (2008) 19714-19719, arXiv: 0810.0415 [q-bio].

7. Predicting the Order in Which Contacts Are Broken during Single Molecule Protein Stretching Experiments
JI Sulkowska, A Kloczkowski, TZ Sen, M Cieplak, RL Jernigan
Proteins: Structure, Function, and Bioinformatics (2008) 71, 45-60.

6. Selection of optimal variants of Go-like models of proteins through studies of stretching
JI Sulkowska, M Cieplak
Biophys. J. (2008) 95, 3174.

5. Tightening of knots in proteins
JI Sulkowska, P Sułkowski, P Szymczak, M Cieplak
Phys. Rev. Lett. (2008) 100, 058106.

2007

4. Mechanical Stretching of proteins – A theoretical survey of the Protein Data Bank
JI Sulkowska, M Cieplak
J. Phys. Cond. Mat. (2007) 19, 283201.

2006

3. Correlated fluctuation of microparticles in viscoelastic solutions: quantitative measurement of materials properties by microrheology in the presence of optical traps
M Atakhorrami, JI Sulkowska, KM Addas, G Koenderink, JX Tang, AJ Levine, FC MacKintosh, CF Schmidt
Phys. Rev. E (2006), 73, 061501.

2005

2. Thermal unfolding of proteins
M Cieplak, JI Sulkowska
J. Chem. Phys. (2005) 123, 194908.

1. Chirality and protein folding
JI Kwiecińska, M Cieplak
J. Phys. Cond. Mat. (2005) 17, S1565.

Miscellanea

15. Radio TokFM, Radiowa Akademia Nauk – YSF Meeting (1015)

14. „EMBO and Poland”, EMBO Encounters, 28 (2014)

13. „Science that matter”, EMBO, Excellence in life sciences (2014)

12. „Polska badaczka chce rozwiązać zagadkę zawęźlonych białek”, PAP (2013)

11. „Knots and slipknot in protein molecules” Math in the Media, USA

11. Radio TokFM, Radiowa Akademia Nauk – Biophysical Society (2013)

10. “Unraveling the Mysteries of Knotted Proteins” Wired (2012)

9. “Protein Knots Gain New Evolutionary Significance” Science Daily (2012)

8. “Protein folding evolved in knotty puzzle” Futurity (2012)

7. “Knotty proteins present new puzzle” press release in UCSB 2012

6. “Better way to predict how protein fold” Futurity (2012)

5. ”Conservation of complex knotting and slipknotting patterns in proteins” press release at Rice University 2012

4. „How to untie?” J. Am. Chem. Soc., Image Challenge (2011)

3. “Protein folding: knotted or not”, Royal Society of Chemistry – Chemistry World News (2010)

2. “Polscy badacze na tropie tajemnic wezlów w bialkach”, MNiSW – Sukcesy uczonych (2010), PAP – Nauka w Polsce (2010)

1. “Jamming proteins with slipknots and their free energy landscape”, Vir. J. Bio. Phys. Res. 19 (2010)

more news 

http://www.biosciencetechnology.com/News/2012/06/Protein-Knots-Gain-New-Evolutionary-Significance